Rendering multiple smoke/fire domains
If you haven't already, you will want to assign a flow group for your smoke domain and place your emitter into a group.

First, select your emitter and assign a group to it (alternative way to group would be to select the emitter, go to the Object tab -> Groups, assign a group and give it a name).

For your smoke domain, under the Physics tab -> Smoke Groups, set the Flow Group to the group you just made. This will prevent mixing of other emitters with that particular domain, allowing multiple domains to be in the same area and layer.

EDIT: One last thing I forgot to mention, make sure each domain has their own material.

And be warned: This may greatly increase render times, so consider placing them on separate layers regardless.